By the sounds of it you must have picked a pretty busy time to travel through the airport however the time it takes to pass security often depends on how many machines are working or have people to operate them.
In theory BAA have employed more staff and extended the central security point however they still dont seem to have got it right. For example the past month or so various faults have occured were doors in the satellite have been broken so in BAA's infinite wisdom they get a security agent to sit by the door to guard it, no problem there you would have though however does it not occur to them......JUST FIX THE DOOR
Then this would free that menber of staff to be useful were they actually need. Times that by the number of faulty doors probably being guarded and you have one more lane at security open.
Secondly the nature of the locos at STN mean that flight arrivals and departures happen in big waves, for example all EZY and FR fleet gone between 6-8 in the morn and with similar flying times across europe all come back at around 11-2 then the really busy time is around 4-8 as many other carriers do their once or twice daily flights into stansted and are in around this time and it is heaving. Bearing in ming whilst i paint the picture of airside we must take into account that whilst there is a 'quiet time' airside the check in queues are growing rapidly and seciruty starts to build up. I hope this gives you a good idea.
As for my opinion maybe stansted is ok ish in size however nature of the 'waves' as described above makes it hard for the system to cope and i would imagine a more constant and steady flow would allow the airport to run more smoothly. However it is not us who dictate, the airlines want to make money and use the aircraft as often as possible so they want to get the flight out asap to maximise its sectors in turn increasing revenue. The wonderful world of STN and the loco's
